Integrating databases for spatial analysis of parasite-host associations and the novel Brazilian dataset.

Incomplete information on parasites, their associated hosts, and their precise geographical location hampers the ability to predict disease emergence in Brazil, a continental-sized country characterised by significant regional disparities. Here, we demonstrate how the NCBI Nucleotide and GBIF databases can be used as complementary databases to study spatially georeferenced parasite-host associations. We also provide a comprehensive dataset of parasites associated with mammal species that occur in Brazil, the Brazilian Mammal Parasite Occurrence Data (BMPO). This dataset integrates wild mammal species' morphological and life-history traits, zoonotic parasite status, and zoonotic microparasite transmission modes. Through meta-networks, comprising interconnected host species linked by shared zoonotic microparasites, we elucidate patterns of zoonotic microparasite dissemination. This approach contributes to wild animal and zoonoses surveillance, identifying and targeting host species accountable for disproportionate levels of parasite sharing within distinct biomes. Moreover, our novel dataset contributes to the refinement of models concerning disease emergence and parasite distribution among host species.

Socioecological vulnerability and the risk of zoonotic disease emergence in Brazil.

In developing countries, outbreaks of zoonotic diseases (ZDs) result from intertwined ecological, socioeconomic, and demographic processes that shape conditions for (i) increased contact between vulnerable human population and wildlife in areas undergoing environmental degradation and (ii) the rapid geographic spread of infections across socially vulnerable regions. In Brazil, recent increases in environmental and social vulnerabilities, amplified by economic and political crises, are potential triggers for outbreaks. We discuss Brazilian features that favor outbreaks and show a novel quantitative method for zoonotic risk assessment. Using data on nine ZDs from 2001 to 2019, we found that the most significant causal variables were vegetation cover and city remoteness. Furthermore, 8 of 27 states presented low-level risk of ZD outbreaks. Given the ZD-bushmeat connection, we identified central hunted mammals that should be surveilled to prevent spillover events. The current challenge is to coordinate intersectoral collaboration for effective One Health management in megadiverse countries with high social vulnerability and growing environmental degradation like Brazil.

Trypanosomatids in Small Mammals of an Agroecosystem in Central Brazil: Another Piece in the Puzzle of Parasite Transmission in an Anthropogenic Landscape.

We surveyed infection by Trypanosoma spp. and Leishmania spp. in small wild mammals from Cumari, Goiás State aiming to investigate the diversity of trypanosomatid in a modified landscape of the Brazilian Cerrado (and possible infection overlapping with canids from the same area). Blood, skin, spleen, and liver samples were collected for parasitological, serological, and molecular assays. Gracilinanus agilis was the most abundant species (N = 70; 48.6%) and it was the only one with patent parasitemia. Characterization by mini-exon and 18SrDNA targets were achieved in 7/10 hemocultures with positive fresh blood examination, which confirmed the T. cruzi infection by Discrete Typing Units (DTU) TcI in single (N = 2) and mixed infections with other DTUs (N = 5). T. rangeli and T. dionisii were detected in skin fragments from Didelphis albiventris and Oecomys cleberi, respectively. G. agilis were found to be infected by L. braziliensis and L. guyanensis, while Leishmania sp. DNA was detected in the liver of Oligoryzomys nigripes and Calomys expulsus. Subpatent infection by T. cruzi and Leishmania sp. was serologically detected in 15% and 9% of the small mammal fauna, respectively. Small mammals from Cumari are included in T. cruzi and Leshmania spp. transmission cycles, showing a higher diversity of trypanosomatid species and/or genotypes than that observed in canids of the same agroecosystem.

Variation in the skull morphometry of four taxonomic units of Thrichomys (Rodentia: Echimyidae), from different Neotropical biomes.

The echimyid rodents of the genus Thrichomys vary considerably in their behavior and feeding ecology, reflecting their occurrence in environments as different as the Caatinga, Cerrado, Pantanal, and Chaco biomes. While the genus was originally classified as monospecific, a number of Thrichomys species have been recognized in recent decades, based on morphometric, cytogenetic, and molecular analyses. While Thrichomys is well studied, the variation found in its cranial morphology is poorly understood, given the taxonomic and ecological complexities of the genus. Using a geometric morphometric approach, we characterized the differences found in the cranial morphology of four Thrichomys taxonomic units, including three established species, Thrichomys apereoides, Thrichomys fosteri, and Thrichomys laurentius, and one operational taxonomic unit (OTU), Thrichomys aff. laurentius. No significant differences were found among these units in cranium size, but significant variation was found in skull shape. The Procrustes distances provided a quantification of the differences in the shape of the skull, with the largest distances being found between T. aff. laurentius and T. fosteri in the dorsal view, and between T. aff. laurentius and T. apereoides in the ventral view. A Discriminant Function Analysis (DFA) with cross-validation determined that the pairings with the highest correct classification were T. aff. laurentius vs. T. apereoides and T. aff. laurentius vs. T. fosteri, in both views. The principal variation in skull shape was found in the posterior region and the zygomatic arch, which may be related to differences in diet.

Community structure and population dynamics of small mammals in an urban-sylvatic interface area in Rio de Janeiro, Brazil

The Atlantic Forest is one of the most disturbed Brazilian biomes, with 183 out of 298 species of mammals occurring in the state of Rio de Janeiro. In this study, we aimed to characterize the diversity, community structure, and habitat use of small mammals in the FIOCRUZ Atlantic Forest Campus (CFMA), including areas of Pedra Branca State Park (PBSP, subunit Pau da Fome), state of Rio de Janeiro. We also compared species diversity and composition between two moments 15 years apart (2001 and 2012-2015) and analyzed the population dynamics of the marsupial Didelphis aurita (Wied-Neuwied, 1826). Small mammal captures were made in different habitats: sylvatic-urban interface areas near human dwellings, disturbed forest, and preserved forest areas. Five marsupial species and four rodent species were captured in both periods. There was a reduction in species richness and β diversity between the two periods, indicating that disturbances in the environment over the years may have affected the small mammal community structure. The most altered environment showed the greatest species richness and abundance, while the forest areas showed the smallest values, which may be explained by the loss of mammal species, mainly specialist species in forested areas. We identified three groups of species according to habitat preferences: one related to environments with a higher density of vegetation in upper strata - Marmosa paraguayana (Tate, 1931) and Monodelphis americana (Müller, 1776), another related to a higher density in lower forest strata - Akodon cursor (Winge, 1887), and another with no association with the investigated habitat variables - D. aurita and Oligoryzomys nigripes (Olfers, 1818). The small mammal community structure showed a low level of nestedness in both sampling periods.[...]

Community structure and population dynamics of small mammals in an urban-sylvatic interface area in Rio de Janeiro, Brazil

The Atlantic Forest is one of the most disturbed Brazilian biomes, with 183 out of 298 species of mammals occurring in the state of Rio de Janeiro. In this study, we aimed to characterize the diversity, community structure, and habitat use of small mammals in the FIOCRUZ Atlantic Forest Campus (CFMA), including areas of Pedra Branca State Park (PBSP, subunit Pau da Fome), state of Rio de Janeiro. We also compared species diversity and composition between two moments 15 years apart (2001 and 2012-2015) and analyzed the population dynamics of the marsupial Didelphis aurita (Wied-Neuwied, 1826). Small mammal captures were made in different habitats: sylvatic-urban interface areas near human dwellings, disturbed forest, and preserved forest areas. Five marsupial species and four rodent species were captured in both periods. There was a reduction in species richness and β diversity between the two periods, indicating that disturbances in the environment over the years may have affected the small mammal community structure. The most altered environment showed the greatest species richness and abundance, while the forest areas showed the smallest values, which may be explained by the loss of mammal species, mainly specialist species in forested areas. We identified three groups of species according to habitat preferences: one related to environments with a higher density of vegetation in upper strata - Marmosa paraguayana (Tate, 1931) and Monodelphis americana (Müller, 1776), another related to a higher density in lower forest strata - Akodon cursor (Winge, 1887), and another with no association with the investigated habitat variables - D. aurita and Oligoryzomys nigripes (Olfers, 1818). The small mammal community structure showed a low level of nestedness in both sampling periods.[...](AU)

A Taxonomic Update of Small Mammal Plague Reservoirs in South America.

Plague is a disease of epidemic potential that may emerge with discontinuous outbreaks. In South America, 50 wild rodent species have been identified as plague reservoirs, in addition to one lagomorph and two marsupials. To review the nomenclature of plague reservoirs, we examined specimens collected in plague foci, carried out new surveys in Brazilian plague regions, and re-evaluated the nomenclature of South American reservoirs on the basis of the current literature. Five of the 15 species involved with plague in Argentina, three of 10 species involved with plague in Bolivia, three of the seven species involved with plague in Peru, five of the nine species involved with plague in Ecuador, and six of the nine species involved with plague in Brazil have undergone taxonomic changes. In the last 20 years, plague cases were recorded in Bolivia, Brazil, Ecuador, and Peru. These four countries have a high rodent species richness in plague foci, a fact that may be decisive for the maintenance of plague in the wild.

A new acanthocephalan species (Archiacanthocephala: Oligacanthorhynchidae) from the crab-eating fox (Cerdocyon thous ) in the Brazilian pantanal wetlands.

A new species of Oligacanthorhynchidae (Acanthocephala) Prosthenorchis cerdocyonis n. sp. is described from 17 specimens collected from the small intestine of the crab-eating fox Cerdocyon thous Linnaeus, 1766 (Canidae: Carnivora) found in the Brazilian Pantanal wetlands. Specimens were studied using light and scanning electron microscopy. Characteristic features distinguishing the new species from others already described are presented, such as size of the body, the position of lemnisci, size of the eggs, host, and geographical distribution. Details of the body surface obtained by scanning electron microscopy, such as the presence of 2 lateral papillae in the proximal region of the proboscis, the presence of barbs in hooks, and a robust and festooned collar, helped to identify the species. Until now, specimens belonging to Prosthenorchis reported from Cerdocyon thous were not identified to species. Furthermore, the new species is the first to be recorded in C. thous found in the Pantanal wetlands.

Distinct Leishmania species infecting wild caviomorph rodents (Rodentia: Hystricognathi) from Brazil.

BACKGROUND: Caviomorph rodents, some of the oldest Leishmania spp. hosts, are widely dispersed in Brazil. Despite both experimental and field studies having suggested that these rodents are potential reservoirs of Leishmania parasites, not more than 88 specimens were analyzed in the few studies of natural infection. Our hypothesis was that caviomorph rodents are inserted in the transmission cycles of Leishmania in different regions, more so than is currently recognized. METHODOLOGY: We investigated the Leishmania infection in spleen fragments of 373 caviomorph rodents from 20 different species collected in five Brazilian biomes in a period of 13 years. PCR reactions targeting kDNA of Leishmania sp. were used to diagnose infection, while Leishmania species identification was performed by DNA sequencing of the amplified products obtained in the HSP70 (234) targeting. Serology by IFAT was performed on the available serum of these rodents. PRINCIPAL FINDINGS: In 13 caviomorph rodents, DNA sequencing analyses allowed the identification of 4 species of the subgenus L. (Viannia): L. shawi, L. guyanensis, L. naiffi, and L. braziliensis; and 1 species of the subgenus L. (Leishmania): L. infantum. These include the description of parasite species in areas not previously included in their known distribution: L. shawi in Thrichomys inermis from Northeastern Brazil and L. naiffi in T. fosteri from Western Brazil. From the four other positive rodents, two were positive for HSP70 (234) targeting but did not generate sequences that enabled the species identification, and another two were positive only in kDNA targeting. CONCLUSIONS/SIGNIFICANCE: The infection rate demonstrated by the serology (51.3%) points out that the natural Leishmania infection in caviomorph rodents is much higher than that observed in the molecular diagnosis (4.6%), highlighting that, in terms of the host species responsible for maintaining Leishmania species in the wild, our current knowledge represents only the "tip of the iceberg."

Population ecology of hantavirus rodent hosts in southern Brazil.

In this study we analyze population dynamics of hantavirus rodent hosts and prevalence of infection over a 2-year period in Southern Brazil, a region with a high incidence of hantavirus pulmonary syndrome. The 14 small mammal species captured were composed of 10 rodents and four marsupials, the six most abundant species being Akodon serrensis, Oxymycterus judex, Akodon montensis, Akodon paranaensis, Oligoryzomys nigripes, and Thaptomys nigrita. These species displayed a similar pattern with increasing population sizes in fall/winter caused by recruitment and both, increase in reproductive activity and higher hantavirus prevalence in spring/summer. Specific associations between A. montensis/Jaborá Virus (JABV) and O. nigripes/Juquitiba-like Virus (JUQV-like) and spillover infections between A. paranaensis/JABV, A. serrensis/JABV, and A. paranaensis/JUQV-like were observed. Spillover infection in secondary hosts seems to play an important role in maintaining JABV and JUQV-like in the hantavirus sylvatic cycle mainly during periods of low prevalence in primary hosts.

The role of historical barriers in the diversification processes in open vegetation formations during the Miocene/Pliocene using an ancient rodent lineage as a model.

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.

Trypanosoma cruzi among wild and domestic mammals in different areas of the Abaetetuba municipality (Pará State, Brazil), an endemic Chagas disease transmission area.

The presence of acute Chagas disease (ACD) due to oral transmission is growing and expanding in several South American countries. Within the Amazon basin, the Abaetetuba municipality has been a site of recurrent cases spanning across distinct landscapes. Because Chagas disease is primarily a zoonotic infection, we compared the enzootic Trypanosoma cruzi transmission cycles in three different environmental areas of Abaetetuba to better understand this new epidemiological situation. Philander opossum was the most abundant mammalian species collected (38% of the collected mammals) with a T. cruzi prevalence of 57%, as determined by hemocultures. Didelphis marsupialis was abundant only in the area with the higher level of environmental disturbance (approximately 42%) and did not yield detectable parasitemia. Despite similarities observed in the composition of the small mammalian fauna and the prevalence of T. cruzi infection among the studied areas, the potential of these hosts to infect vectors differed significantly according to the degree of land use (with prevalences of 5%, 41%, and 64% in areas A3, A1 and A2, respectively). Domestic mammals were also found to be infected, and one canine T. cruzi isolate was obtained. Our data demonstrated that the transmission of T. cruzi in the Amazon basin is far more complex than had been previously taught and showed that the probability of humans and domestic mammals coming into contact with infected bugs can vary dramatically, even within the same municipality. The exposure of dogs to T. cruzi infection (indicated by positive serology) was the common feature among the studied localities, stressing the importance of selecting domestic mammals as sentinels in the identification of T. cruzi transmission hotspots.

Scapteromys aquaticus (Rodentia: Sigmodontinae) in Brazil with comments on karyotype and phylogenetics relationships

The swamp rats are distributed in Argentina, southern Paraguay, Uruguay and southern Brazil, with two species currently accepted: Scapteromys aquaticus Thomas, 1920 and Scapteromys tumidus Waterhouse, 1837. While S. aquaticus occurs in Argentina, Paraguay and western Uruguay, S. tumidus occurs in Brazil and Uruguay. Here we report for the first time the occurrence of S. aquaticus in gallery forest remnants in Southern Brazil. Karyologic analysis showed 2n = 32 and FNa = 40. Phylogenetic analyses, based on DNA sequences from the mitochondrial cytochrome-b gene indicate that the Brazilian and the Argentinian specimens of S. aquaticus shared one haplotype, while median joining analysis showed lack of population structure. This register, plus the karyotype data available for Brazilian population, recovered four karyomorphotypes in Brazil, corresponding to the two known species of Scapteromys and two unnamed species. This scenario indicates that more multidisciplinary studies are necessary to understand the actual diversity of Scapteromys.

Scapteromys aquaticus (Rodentia: Sigmodontinae) in Brazil with comments on karyotype and phylogenetics relationships

The swamp rats are distributed in Argentina, southern Paraguay, Uruguay and southern Brazil, with two species currently accepted: Scapteromys aquaticus Thomas, 1920 and Scapteromys tumidus Waterhouse, 1837. While S. aquaticus occurs in Argentina, Paraguay and western Uruguay, S. tumidus occurs in Brazil and Uruguay. Here we report for the first time the occurrence of S. aquaticus in gallery forest remnants in Southern Brazil. Karyologic analysis showed 2n = 32 and FNa = 40. Phylogenetic analyses, based on DNA sequences from the mitochondrial cytochrome-b gene indicate that the Brazilian and the Argentinian specimens of S. aquaticus shared one haplotype, while median joining analysis showed lack of population structure. This register, plus the karyotype data available for Brazilian population, recovered four karyomorphotypes in Brazil, corresponding to the two known species of Scapteromys and two unnamed species. This scenario indicates that more multidisciplinary studies are necessary to understand the actual diversity of Scapteromys.(AU)

Hantavirus infection prevalence in wild rodents and human anti-hantavirus serological profiles from different geographic areas of South Brazil.

Paraná state presents the fourth highest number of accumulated cases of hantavirus pulmonary syndrome in Brazil. To map the risk areas for hantavirus transmission we carried out a study based on rodent trapping and determined the anti-hantavirus seroprevalence in these animals and in the inhabitants of these localities. Overall seroprevalence in rodents and humans were 2.5% and 2.4%, respectively. Eighty-two percent of the seropositive rodents were genetically analyzed. Phylogenetic analyses revealed that hantaviruses from rodent samples cluster with Araucária (Juquitiba-like) or Jaborá hantavirus genotypes. The Jaborá strain was identified in Akodon serrensis and Akodon montensis, whereas the Araucária strain was detected in Oligoryzomys nigripes, Oxymycterus judex, A. montensis, and Akodon paranaensis, with the latter species being identified for the first time as a natural host. These findings expose the complex relationships between virus and reservoirs in Brazil, which could have an impact on hantavirus transmission dynamics in nature and human epidemiology.

Investigation of Chagas disease in four periurban areas in northeastern Brazil: epidemiologic survey in man, vectors, non-human hosts and reservoirs.

Chagas disease was investigated in four periurban areas of Ceará state, northeastern Brazil, through serological, parasitological and molecular methods in humans, reservoirs and vectors. A cross-sectional survey revealed a seroprevalence rate of 1.2% (13/1076 residents, six also proving positive through PCR). Trypanosoma cruzi infection was not detected in children under 10 years old. Triatoma pseudomaculata prevailed in the peridomiciles: 63 specimens, 69% (34/49) infected with trypanosomatids. Rhodnius nasutus was captured in Copernicia prunifera palm trees (n=280; 25.0% infected with trypanosomatids) and inside dwellings (n=8, all uninfected). Trypanosoma cruzi seropositive reservoirs, represented by Didelphis albiventris (n=27), Rattus rattus (n=24), Thrichomys laurentius (n=2), Mus musculus (n=1) and Monodelphis domestica (n=1), were identified. Among domestic dogs (n=96) seroprevalence reached 21.9%. Miniexon multiplex PCR assays characterized TcI in triatomines. Both TcI and TcII were detected in wild mammal hosts. We conclude that Trypanosoma cruzi circulates within a domestic zoonotic cycle, requiring continuous surveillance. Insecticide application to domiciles does not appear to prevent continuous reintroduction of wild triatomine specimens, presenting a challenge to authorities involved in Chagas disease control.

Colonization process of the Brazilian common vesper mouse, Calomys expulsus (Cricetidae, Sigmodontinae): a biogeographic hypothesis.

Riverine barriers have been associated to genetic diversification and speciation of several taxa. The Rio São Francisco is one of the largest rivers in South America, representing the third largest river basin in Brazil and operating as a geographic barrier to gene flow of different taxa. To evaluate the influence of the Rio São Francisco in the speciation of small rodents, we investigated the genetic structure of Calomys expulsus with phylogenetic and network analyses of cytochrome b DNA. Our results suggested that C. expulsus can be divided into 3 subpopulations, 2 on the left and another one on the right bank of this river. The time of divergence of these subpopulations, using a Bayesian framework, suggested colonization from the south to the north/northeast. Spatial analysis using a clustering method and the Monmonier's algorithm suggested that the Rio São Francisco is a biogeographic barrier to gene flow and indicated that this river may play a role in the incipient speciation process of these subpopulations.

Genetic characterization of hantaviruses associated with sigmodontine rodents in an endemic area for hantavirus pulmonary syndrome in southern Brazil.

An ecological assessment of reservoir species was conducted in a rural area (Jaborá) in the mid-west of the state of Santa Catarina in southern Brazil, where hantavirus pulmonary syndrome is endemic, to evaluate the prevalence of hantavirus infection in wild rodents. Blood and tissue samples were collected from 507 rodents during seven field trips from March 2004 to April 2006. Some of the animals were karyotyped to confirm morphological identification. Phylogenetic reconstructions of rodent specimens, based on the mitochondrial DNA cytochrome b gene sequences, were also obtained. Hantavirus antibody was found in 22 (4.3%) of the 507 rodents: 5 Akodon montensis, 2 Akodon paranaensis, 14 Oligoryzomys nigripes, and 1 Sooretamys angouya. Viral RNAs detected in O. nigripes and A. montensis were amplified and sequenced. O. nigripes virus genome was 97.5% (nt) and 98.4% (nt) identical to sequences published for Araucaria (Juquitiba-like) virus based on N and G2 fragment sequences. Viral sequences from A. montensis strain showed 89% and 88% nucleotide identities in a 905-nt fragment of the nucleocapsid (N) protein-coding region of the S segment when it was compared with two other Akodontine rodent-associated viruses from Paraguay, A. montensis and Akodon cursor, respectively. Phylogenetic analysis showed the cocirculation of two genetic hantavirus lineages in the state of Santa Catarina, one from O. nigripes and the other from A. montensis, previously characterized in Brazil and Paraguay, respectively. The hantavirus associated with A. montensis, designed Jaborá virus, represents a distinct phylogenetic lineage among the Brazilian hantaviruses.

Hantaviruses and hantavirus pulmonary syndrome, Maranhao, Brazil.

To confirm circulation of Anajatuba virus in Maranhao, Brazil, we conducted a serologic survey (immunoglobulin G ELISA) and phylogenetic studies (nucleocapsid gene sequences) of hantaviruses from wild rodents and persons with hantavirus pulmonary syndrome. This virus is transmitted by Oligoryzomys fornesi rodents and is responsible for hantavirus pulmonary syndrome in this region.

Phylogenetic characterization of hantaviruses from wild rodents and hantavirus pulmonary syndrome cases in the state of Parana (southern Brazil).

Over 1,100 cases of hantavirus pulmonary syndrome (HPS) have occurred in Brazil since 1993, but little is known about Brazilian hantaviruses, and many of their rodent hosts remain unknown. The Araucaria hantavirus (ARAUV) was described recently from HPS patients from Paraná, in southern Brazil, but its host could not be identified. In this study, rodents were captured from regions with high HPS prevalence to address this issue. ARAUV RNA was detected in three distantly related rodent species: Oligoryzomys nigripes, Oxymycterus judex and Akodon montensis. Furthermore, a specimen of A. montensis was infected with a Jaborá-like virus, implying that A. montensis can be infected by at least two different hantaviruses. The presence of the same hantavirus strain in three different rodent species and the co-circulation of two different strains in the same rodent species highlight the potential for genomic reassortment, which could have an impact on hantavirus transmission dynamics in nature and on human epidemiology.